-
1
-
-
84975795680
-
An integrated map of genetic variation from 1,092 human genomes
-
Abecasis, G. R., A. Auton, L. D. Brooks, M. A. DePristo, R. M. Durbin et al., 2012 An integrated map of genetic variation from 1,092 human genomes. Nature 491: 56–65.
-
(2012)
Nature
, vol.491
, pp. 56-65
-
-
Abecasis, G.R.1
Auton, A.2
Brooks, L.D.3
Depristo, M.A.4
Durbin, R.M.5
-
2
-
-
84970015769
-
FINEMAP: Efficient variable selection using summary data from genome-wide association studies
-
Benner, C., C. C. Spencer, A. S. Havulinna, V. Salomaa, S. Ripatti et al., 2016 FINEMAP: efficient variable selection using summary data from genome-wide association studies. Bioinformatics 32: 1493–1501.
-
(2016)
Bioinformatics
, vol.32
, pp. 1493-1501
-
-
Benner, C.1
Spencer, C.C.2
Havulinna, A.S.3
Salomaa, V.4
Ripatti, S.5
-
3
-
-
84872395684
-
Regional activation of the cancer genome by long-range epigenetic remodeling
-
Bert, S. A., M. D. Robinson, D. Strbenac, A. L. Statham, J. Z. Song et al., 2013 Regional activation of the cancer genome by long-range epigenetic remodeling. Cancer Cell 23: 9–22.
-
(2013)
Cancer Cell
, vol.23
, pp. 9-22
-
-
Bert, S.A.1
Robinson, M.D.2
Strbenac, D.3
Statham, A.L.4
Song, J.Z.5
-
5
-
-
84887281556
-
Integrated enrichment analysis of variants and pathways in genome-wide association studies indicates central role for IL-2 signaling genes in type 1 diabetes, and cytokine signaling genes in Crohn’s disease
-
Carbonetto, P., and M. Stephens, 2013 Integrated enrichment analysis of variants and pathways in genome-wide association studies indicates central role for IL-2 signaling genes in type 1 diabetes, and cytokine signaling genes in Crohn’s disease. PLoS Genet. 9: e1003770.
-
(2013)
Plos Genet
, vol.9
-
-
Carbonetto, P.1
Stephens, M.2
-
6
-
-
84907851533
-
PedBLIMP: Extending linear predictors to impute genotypes in pedigrees
-
Chen, W., and D. J. Schaid, 2014 PedBLIMP: extending linear predictors to impute genotypes in pedigrees. Genet. Epidemiol. 38: 531–541.
-
(2014)
Genet. Epidemiol
, vol.38
, pp. 531-541
-
-
Chen, W.1
Schaid, D.J.2
-
7
-
-
84937035185
-
Fine mapping causal variants with an approximate bayesian method using marginal test statistics
-
Chen, W., B. R. Larrabee, I. G. Ovsyannikova, R. B. Kennedy, I. H. Haralambieva et al., 2015 Fine mapping causal variants with an approximate bayesian method using marginal test statistics. Genetics 200: 719–736.
-
(2015)
Genetics
, vol.200
, pp. 719-736
-
-
Chen, W.1
Larrabee, B.R.2
Ovsyannikova, I.G.3
Kennedy, R.B.4
Haralambieva, I.H.5
-
8
-
-
84888343067
-
Androgen regulation of the TMPRSS2 gene and the effect of a SNP in an androgen response element
-
Clinckemalie, L., L. Spans, V. Dubois, M. Laurent, C. Helsen et al., 2013 Androgen regulation of the TMPRSS2 gene and the effect of a SNP in an androgen response element. Mol. Endocrinol. 27: 2028–2040.
-
(2013)
Mol. Endocrinol
, vol.27
, pp. 2028-2040
-
-
Clinckemalie, L.1
Spans, L.2
Dubois, V.3
Laurent, M.4
Helsen, C.5
-
9
-
-
84857707318
-
ChromHMM: Automating chromatin-state discovery and characterization
-
Ernst, J., and M. Kellis, 2012 ChromHMM: automating chromatin-state discovery and characterization. Nat. Methods 9: 215– 216.
-
(2012)
Nat. Methods
, vol.9
-
-
Ernst, J.1
Kellis, M.2
-
10
-
-
84926632357
-
Large-scale imputation of epige-nomic datasets for systematic annotation of diverse human tissues
-
Ernst, J., and M. Kellis, 2015 Large-scale imputation of epige-nomic datasets for systematic annotation of diverse human tissues. Nat. Biotechnol. 33: 364–376.
-
(2015)
Nat. Biotechnol
, vol.33
, pp. 364-376
-
-
Ernst, J.1
Kellis, M.2
-
11
-
-
77950537175
-
Regularization paths for generalized linear models via coordinate descent
-
Friedman, J., T. Hastie, and R. Tibshirani, 2010 Regularization paths for generalized linear models via coordinate descent. J. Stat. Softw. 33: 1–22.
-
(2010)
J. Stat. Softw
, vol.33
, pp. 1-22
-
-
Friedman, J.1
Hastie, T.2
Tibshirani, R.3
-
12
-
-
84856321864
-
Dissecting the regulatory architecture of gene expression QTLs
-
Gaffney, D. J., J. B. Veyrieras, J. F. Degner, R. Pique-Regi, A. A. Pai et al., 2012 Dissecting the regulatory architecture of gene expression QTLs. Genome Biol. 13: R7.
-
(2012)
Genome Biol
, vol.13
, pp. 7
-
-
Gaffney, D.J.1
Veyrieras, J.B.2
Degner, J.F.3
Pique-Regi, R.4
Pai, A.A.5
-
13
-
-
58149175796
-
Practical issues in imputation-based association mapping
-
Guan, Y., and M. Stephens, 2008 Practical issues in imputation-based association mapping. PLoS Genet. 4: e1000279.
-
(2008)
Plos Genet
, vol.4
-
-
Guan, Y.1
Stephens, M.2
-
14
-
-
82955223524
-
Bayesian variable selection regression for genome-wide association studies and other large-scale problems
-
Guan, Y. T., and M. Stephens, 2011 Bayesian variable selection regression for genome-wide association studies and other large-scale problems. Ann. Appl. Stat. 5: 1780–1815.
-
(2011)
Ann. Appl. Stat
, vol.5
, pp. 1780-1815
-
-
Guan, Y.T.1
Stephens, M.2
-
15
-
-
84922273141
-
Partitioning heritability of regulatory and cell-type-specific variants across 11 common diseases
-
Gusev, A., S. H. Lee, G. Trynka, H. Finucane, B. J. Vilhjalmsson et al., 2014 Partitioning heritability of regulatory and cell-type-specific variants across 11 common diseases. Am. J. Hum. Genet. 95: 535–552.
-
(2014)
Am. J. Hum. Genet
, vol.95
, pp. 535-552
-
-
Gusev, A.1
Lee, S.H.2
Trynka, G.3
Finucane, H.4
Vilhjalmsson, B.J.5
-
16
-
-
84896695503
-
Comprehensive functional annotation of 77 prostate cancer risk loci
-
Hazelett, D. J., S. K. Rhie, M. Gaddis, C. Yan, D. L. Lakeland et al., 2014 Comprehensive functional annotation of 77 prostate cancer risk loci. PLoS Genet. 10: e1004102.
-
(2014)
Plos Genet
, vol.10
-
-
Hazelett, D.J.1
Rhie, S.K.2
Gaddis, M.3
Yan, C.4
Lakeland, D.L.5
-
17
-
-
77950262538
-
Nucleosome dynamics define transcriptional enhancers
-
He, H. H., C. A. Meyer, H. Shin, S. T. Bailey, G. Wei et al., 2010 Nucleosome dynamics define transcriptional enhancers. Nat. Genet. 42: 343–347.
-
(2010)
Nat. Genet
, vol.42
, pp. 343-347
-
-
He, H.H.1
Meyer, C.A.2
Shin, H.3
Bailey, S.T.4
Wei, G.5
-
18
-
-
84875448918
-
Integrative annotation of chromatin elements from ENCODE data
-
Hoffman, M. M., J. Ernst, S. P. Wilder, A. Kundaje, R. S. Harris et al., 2013 Integrative annotation of chromatin elements from ENCODE data. Nucleic Acids Res. 41: 827–841.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. 827-841
-
-
Hoffman, M.M.1
Ernst, J.2
Wilder, S.P.3
Kundaje, A.4
Harris, R.S.5
-
19
-
-
84908042860
-
Identifying causal variants at loci with multiple signals of association
-
Hormozdiari, F., E. Kostem, E. Y. Kang, B. Pasaniuc, and E. Eskin, 2014 Identifying causal variants at loci with multiple signals of association. Genetics 198: 497–508.
-
(2014)
Genetics
, vol.198
, pp. 497-508
-
-
Hormozdiari, F.1
Kostem, E.2
Kang, E.Y.3
Pasaniuc, B.4
Eskin, E.5
-
21
-
-
84908324508
-
Integrating functional data to prioritize causal variants in statistical fine-mapping studies
-
Kichaev, G., W. Y. Yang, S. Lindstrom, F. Hormozdiari, E. Eskin et al., 2014 Integrating functional data to prioritize causal variants in statistical fine-mapping studies. PLoS Genet. 10: e1004722.
-
(2014)
Plos Genet
, vol.10
-
-
Kichaev, G.1
Yang, W.Y.2
Lindstrom, S.3
Hormozdiari, F.4
Eskin, E.5
-
22
-
-
78049484065
-
Penalized regression, standard errors, and Bayesian lassos
-
Kyung, M., J. Gill, M. Ghosh, and G. Casella, 2010 Penalized regression, standard errors, and Bayesian lassos. Bayesian Anal. 5: 369–411.
-
(2010)
Bayesian Anal
, vol.5
, pp. 369-411
-
-
Kyung, M.1
Gill, J.2
Ghosh, M.3
Casella, G.4
-
23
-
-
84865822182
-
Systematic localization of common disease-as-sociated variation in regulatory DNA
-
Maurano, M. T., R. Humbert, E. Rynes, R. E. Thurman, E. Haugen et al., 2012 Systematic localization of common disease-as-sociated variation in regulatory DNA. Science 337: 1190– 1195.
-
(2012)
Science
, vol.337
-
-
Maurano, M.T.1
Humbert, R.2
Rynes, E.3
Thurman, R.E.4
Haugen, E.5
-
24
-
-
37249080278
-
Penalized logistic regression for detecting gene interactions
-
Park, M. Y., and T. Hastie, 2008 Penalized logistic regression for detecting gene interactions. Biostatistics 9: 30–50.
-
(2008)
Biostatistics
, vol.9
, pp. 30-50
-
-
Park, M.Y.1
Hastie, T.2
-
25
-
-
84921782559
-
Fast and accurate imputation of summary statistics enhances evidence of functional enrichment
-
Pasaniuc, B., N. Zaitlen, H. Shi, G. Bhatia, A. Gusev et al., 2014 Fast and accurate imputation of summary statistics enhances evidence of functional enrichment. Bioinformatics 30: 2906–2914.
-
(2014)
Bioinformatics
, vol.30
, pp. 2906-2914
-
-
Pasaniuc, B.1
Zaitlen, N.2
Shi, H.3
Bhatia, G.4
Gusev, A.5
-
26
-
-
84898723939
-
Joint analysis of functional genomic data and genome-wide association studies of 18 human traits
-
Pickrell, J. K., 2014 Joint analysis of functional genomic data and genome-wide association studies of 18 human traits. Am. J. Hum. Genet. 94: 559–573.
-
(2014)
Am. J. Hum. Genet
, vol.94
, pp. 559-573
-
-
Pickrell, J.K.1
-
27
-
-
84887187386
-
Integrative variable selection via Bayesian model uncertainty
-
Quintana, M. A., and D. V. Conti, 2013 Integrative variable selection via Bayesian model uncertainty. Stat. Med. 32: 4938–4953.
-
(2013)
Stat. Med
, vol.32
, pp. 4938-4953
-
-
Quintana, M.A.1
Conti, D.V.2
-
28
-
-
34547622688
-
Imputation-based analysis of association studies: Candidate regions and quantitative traits
-
Servin, B., and M. Stephens, 2007 Imputation-based analysis of association studies: candidate regions and quantitative traits. PLoS Genet. 3: e114.
-
(2007)
Plos Genet
, vol.3
-
-
Servin, B.1
Stephens, M.2
-
29
-
-
84872391385
-
The androgen receptor induces a distinct transcriptional program in castration-resistant prostate cancer in man
-
Sharma, N. L., C. E. Massie, A. Ramos-Montoya, V. Zecchini, H. E. Scott et al., 2013 The androgen receptor induces a distinct transcriptional program in castration-resistant prostate cancer in man. Cancer Cell 23: 35–47.
-
(2013)
Cancer Cell
, vol.23
, pp. 35-47
-
-
Sharma, N.L.1
Massie, C.E.2
Ramos-Montoya, A.3
Zecchini, V.4
Scott, H.E.5
-
30
-
-
79961193174
-
HAPGEN2: Simulation of multiple disease SNPs
-
Su, Z., J. Marchini, and P. Donnelly, 2011 HAPGEN2: simulation of multiple disease SNPs. Bioinformatics 27: 2304–2305.
-
(2011)
Bioinformatics
, vol.27
, pp. 2304-2305
-
-
Su, Z.1
Marchini, J.2
Donnelly, P.3
-
31
-
-
84907196865
-
Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer
-
Taberlay, P. C., A. L. Statham, T. K. Kelly, S. J. Clark, and P. A. Jones, 2014 Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer. Genome Res. 24: 1421– 1432.
-
(2014)
Genome Res
, vol.24
-
-
Taberlay, P.C.1
Statham, A.L.2
Kelly, T.K.3
Clark, S.J.4
Jones, P.A.5
-
32
-
-
84918539838
-
CtBP2 modulates the androgen receptor to promote prostate cancer progression
-
Takayama, K., T. Suzuki, T. Fujimura, T. Urano, S. Takahashi et al., 2014 CtBP2 modulates the androgen receptor to promote prostate cancer progression. Cancer Res. 74: 6542–6553.
-
(2014)
Cancer Res
, vol.74
, pp. 6542-6553
-
-
Takayama, K.1
Suzuki, T.2
Fujimura, T.3
Urano, T.4
Takahashi, S.5
-
33
-
-
84863072810
-
Integration of regulatory networks by NKX3–1 promotes androgen-dependent prostate cancer survival
-
Tan, P. Y., C. W. Chang, K. R. Chng, K. D. Wansa, W. K. Sung et al., 2012 Integration of regulatory networks by NKX3–1 promotes androgen-dependent prostate cancer survival. Mol. Cell. Biol. 32: 399–414.
-
(2012)
Mol. Cell. Biol
, vol.32
, pp. 399-414
-
-
Tan, P.Y.1
Chang, C.W.2
Chng, K.R.3
Wansa, K.D.4
Sung, W.K.5
-
34
-
-
77955505564
-
Biological, clinical and population relevance of 95 loci for blood lipids
-
Teslovich, T. M., K. Musunuru, A. V. Smith, A. C. Edmondson, I. M. Stylianou et al., 2010 Biological, clinical and population relevance of 95 loci for blood lipids. Nature 466: 707–713.
-
(2010)
Nature
, vol.466
, pp. 707-713
-
-
Teslovich, T.M.1
Musunuru, K.2
Smith, A.V.3
Edmondson, A.C.4
Stylianou, I.M.5
-
35
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
The ENCODE Project Consortium
-
The ENCODE Project Consortium, 2012 An integrated encyclopedia of DNA elements in the human genome. Nature 489: 57–74.
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
-
36
-
-
84948680539
-
Identification of candidate genes for prostate cancer-risk SNPs utilizing a normal prostate tissue eQTL data set
-
Thibodeau, S. N., A. J. French, S. K. McDonnell, J. Cheville, S. Middha et al., 2015 Identification of candidate genes for prostate cancer-risk SNPs utilizing a normal prostate tissue eQTL data set. Nat. Commun. 6: 8653.
-
(2015)
Nat. Commun
, vol.6
, pp. 8653
-
-
Thibodeau, S.N.1
French, A.J.2
McDonnell, S.K.3
Cheville, J.4
Middha, S.5
-
37
-
-
85194972808
-
Regression shrinkage and selection via the Lasso
-
Tibshirani, R., 1996 Regression shrinkage and selection via the Lasso. J. R. Stat. Soc. B 58: 267–288.
-
(1996)
J. R. Stat. Soc. B
, vol.58
, pp. 267-288
-
-
Tibshirani, R.1
-
38
-
-
84872012577
-
Degrees of freedom in lasso problems
-
Tibshirani, R. J., and J. Taylor, 2012 Degrees of freedom in lasso problems. Ann. Stat. 40: 1198–1232.
-
(2012)
Ann. Stat
, vol.40
, pp. 1198-1232
-
-
Tibshirani, R.J.1
Taylor, J.2
-
39
-
-
66049114148
-
Bayes factors for genome-wide association studies: Comparison with P-values
-
Wakefield, J., 2009 Bayes factors for genome-wide association studies: comparison with P-values. Genet. Epidemiol. 33: 79– 86.
-
(2009)
Genet. Epidemiol
, vol.33
-
-
Wakefield, J.1
-
40
-
-
79959198166
-
Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA
-
Wang, D., I. Garcia-Bassets, C. Benner, W. Li, X. Su et al., 2011 Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA. Nature 474: 390–394.
-
(2011)
Nature
, vol.474
, pp. 390-394
-
-
Wang, D.1
Garcia-Bassets, I.2
Benner, C.3
Li, W.4
Su, X.5
-
41
-
-
84861461948
-
Using linear predictors to impute allele frequencies from summary or pooled genotype data
-
Wen, X., and M. Stephens, 2010 Using linear predictors to impute allele frequencies from summary or pooled genotype data. Ann. Appl. Stat. 4: 1158–1182.
-
(2010)
Ann. Appl. Stat
, vol.4
, pp. 1158-1182
-
-
Wen, X.1
Stephens, M.2
-
42
-
-
84930368286
-
Cross-population joint analysis of eQTLs: Fine mapping and functional annotation
-
Wen, X., F. Luca, and R. Pique-Regi, 2015 Cross-population joint analysis of eQTLs: fine mapping and functional annotation. PLoS Genet. 11: e1005176.
-
(2015)
Plos Genet
, vol.11
-
-
Wen, X.1
Luca, F.2
Pique-Regi, R.3
-
43
-
-
84874783818
-
Polygenic modeling with bayesian sparse linear mixed models
-
Zhou, X., P. Carbonetto, and M. Stephens, 2013 Polygenic modeling with bayesian sparse linear mixed models. PLoS Genet. 9: e1003264.
-
(2013)
Plos Genet
, vol.9
-
-
Zhou, X.1
Carbonetto, P.2
Stephens, M.3
-
44
-
-
84994873942
-
Bayesian large-scale multiple regression with summary statistics from genome-wide association studies
-
Zhu, X., and M. Stephens, 2016 Bayesian large-scale multiple regression with summary statistics from genome-wide association studies. bioRxiv, DOI: http://dx.doi.org/10.1101/042457.
-
(2016)
BioRxiv
-
-
Zhu, X.1
Stephens, M.2
-
45
-
-
16244401458
-
Regularization and variable selection via the elastic net
-
Zou, H., and T. Hastie, 2005 Regularization and variable selection via the elastic net. J. R. Stat. Soc. Series B Stat. Methodol. 67: 301–320.
-
(2005)
J. R. Stat. Soc. Series B Stat. Methodol
, vol.67
, pp. 301-320
-
-
Zou, H.1
Hastie, T.2
|